Identification and characterization of rice blast resistance gene Pid4 by a combination of transcriptomic profiling and genome analysis

Chen, Zhixiong; Zhao, Wen; Zhu, Xiaobo; Zou, Chengdong; Yin, Junjie; Chern, Mawsheng; Zhao, Xiaogang; Ying, Heng; Jiang, Xin; Li, Yongzhen; Liao, Haicheng; Cheng, Mengping; Li, Weitao; He, Min; Wang, Jing; Ma, Bo; Wang, Jirui; Li, Shigui; Zhu, Lihuang; Chen, Xuewei

doi:10.1016/j.jgg.2018.10.007

Cited by 28 publications

(15 citation statements)

References 59 publications

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“…The search on RAP-DB detected a total of 26 genes located in the chromosome 6 interval from 10,084,497 to 10,490,006 bp. Of these, 20 were functionally annotated and included Os06g0286700 (from 10,387,793 to 10,390,465 bp), corresponding to the cloned blast R gene Piz and its allelic variants Piz-t, Pi2, Pi9 and Pi40 (Zhou et al 2006 ; Wang et al 2017 ) , and Os06g0287500, corresponding to Pid4 (from 10,435,819 to 10,441,907 bp; Chen et al 2018 ) both closely proximal to the BRGC06 peak marker (at 10,390,066 bp; Fig. 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, Piz can be suggested as the most probable candidate gene for this region. The Pid4 blast resistance gene (Os06g0287500) is also localized on chromosome 6, inside the BRF06–1 and BRG06 MTAs (from 10.435.819 to 10.441.907 bp; Chen et al 2018 ). Pid4 encodes a a typical CC-NB-LRR protein localized in both nucleus and cytoplasm and was constitutively expressed in uninfected plants (Chen et al 2018 ).…”

Section: Discussionmentioning

confidence: 99%

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Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Volante

Tondelli²,

Desiderio³

et al. 2020

Rice

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Background Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. Results The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11–2 and BRGC11–3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. Conclusions We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Volante

Tondelli²,

Desiderio³

et al. 2020

Rice

View full text Add to dashboard Cite

show abstract

“…Therefore, Piz can be suggested as the most probable candidate gene for this region. The Pid4 blast resistance gene (Os06g0287500) is also localized on chromosome 6, inside the BRF06-1 and BRG06 MTAs (from 10.435.819 to 10.441.907 bp; Chen et al 2018). Pid4 encodes a a typical CC-NB-LRR protein localized in both nucleus and cytoplasm and was constitutively expressed in uninfected plants .…”

Section: Discussionmentioning

confidence: 99%

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Volante¹,

Tondelli

Desiderio

et al. 2020

Preprint

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Background Rice blast, caused by the fungus Pyricularia oryzae , represents the most damaging fungal disease of rice worldwide. Utilization of resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different blast strains. Results The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs no obvious candidates or positional relationships were identified, raising the possibility that these loci harbor previously unidentified blast resistance genes. Conclusions We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.

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“…With improvements in technology, the cloning and exploitation of rice-blast R genes has seen tremendous progress in the twentyfirst century. To date, 119 blast R-genes and more than 400 quantitative trait loci (QTLs) have been mapped, and more than 30 blast-resistance genes have been mapped and cloned (Balliniet et al, 2008;Bryan et al, 2000;Chen et al, 2018a;Chen et al, 2006;Chen et al, 2018b;Fukuoka et al, 2009;Inoue et al, 2017;Hayashi et al, 2010;Ishihara et al, 2014;Li et al, 2017;Lin et al, 2007;Liu et al, 2002;Liu et al, 2007;Zhao et al, 2018).…”

Section: Current Status Of Cloning and Characterization Of Rice Blastmentioning

confidence: 99%

Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

Zhou

Lei

Wang

et al. 2020

Rice

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Background As rice (Oryza sativa) is the staple food of more than half the world’s population, rice production contributes greatly to global food security. Rice blast caused by the fungus Magnaporthe oryzae (M. oryzae) is a devastating disease that affects rice yields and grain quality, resulting in substantial economic losses annually. Because the fungus evolves rapidly, the resistance conferred by most the single blast-resistance genes is broken after a few years of intensive agricultural use. Therefore, effective resistance breeding in rice requires continual enrichment of the reservoir of resistance genes, alleles, or QTLs. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles. Results We carried out a large-scale screen for novel blast-resistance alleles in 1883 rice varieties from major rice-producing areas across China. Of these, 361 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. We used sequence-based allele mining to amplify and sequence the allelic variants of the major rice blast-resistance genes at the Pi2/Pi9 locus of chromosome 6 from the 361 blast-resistant varieties, and the full-length coding region of this gene could be amplified from 107 varieties. Thirteen novel Pi9 alleles (named Pi9-Type1 to Pi9-Type13) were identified in these 107 varieties based on comparison to the Pi9 referenced sequence. Based on the sequencing results, the Pi2/Pi9 locus of the 107 varieties was divided into 15 genotypes (including three different genotypes of Pi9-Type5). Fifteen varieties, each representing one genotype, were evaluated for resistance to 34 M. oryzae isolates. The alleles from seven varieties with the highest resistance and widest resistance spectra were selected for transformation into the susceptible variety J23B to construct near-isogenic lines (NILs). These NILs showed resistance in a field test in Enshi and Yichang, indicating that the seven novel rice blast-resistance tandem-repeat regions at the Pi2/Pi9 locus of chromosome 6 could potentially serve as a genetic resource for molecular breeding of resistance to rice blast. Conclusions The thirteen novel Pi9 alleles identified in this study expand the list of available of blast-resistance alleles. Seven tandem-repeat regions of the Pi2/Pi9 locus from different donors were characterized as broad-spectrum rice blast-resistance fragments; these donors enrich the genetic resources available for rice blast-resistance breeding programs.

show abstract

Identification and characterization of rice blast resistance gene Pid4 by a combination of transcriptomic profiling and genome analysis

Cited by 28 publications

References 59 publications

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining

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